You can analyse your hits with DSSP to see the secondary structure afterwards.
Cheers,
Robbie
On 19 Oct 2021 21:58, Guillaume Gaullier <guillaume.gaull...@icm.uu.se> wrote:
Hello,
ScanProsite almost does what you want, but since it only searches sequence databases, it has no notion of secondary structures and therefore cannot exclude motifs found in a secondary structure.https://prosite.expasy.org/scanprosite/
I don’t know of any tool that would search structures and not only sequences. But if your motif isn’t too short or simple, ScanProsite should return a small enough number of hits that you could then inspect structures (or AlphaFold models) manually.
I hope this helps,
Guillaume
On 19 Oct 2021, at 20:43, Jan van Agthoven <janc...@gmail.com> wrote:
Dear all,I apologize for the off-topic question. I’d like to search for a particular aa sequence motif inside the protein sequence data bank (Swiss-prot, Uniprot, etc…) with the following criteria:
- It should not be inside a secondary structure.
Does anyone know a program that could do that?Thanks,Jan
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